Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any of them, So if it has counted it (Hbond b/w same donor and acceptor but with different hydrogen) twice in one calculation then it will be counted twice in another, So wont the result with/without nomerge be the same?
The difference is 4-5 Hbonds.. Thank you Kavya On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund <[email protected]> wrote: > Hi. What version was this? Have you tried with -nomerge? > > Erik > > > On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: > > Dear users, >> >> While calculating hydrogen bonds for a simulation, it >> was found that the average number of intra protein >> hbonds was not equal to sum of MM, MS and SS >> hydrogen bonds. (MM - main chain - main chain, >> MS - main chain - side chain and side chain - side >> chain hydrogen bonds). There was a difference of 5 >> or so hbonds between intra-protein and MM+MS+SS >> hbonds. why is this so? >> I selected the options 7 7 for MM, 7 8 for MS and 8 8 >> for SS hydrogen bonds. >> >> One clarification. nhbdist option gives 0, 1, 2, 3 and >> total hydrogen bonds per hydrogen. Does this mean >> that a single hydrogen involving in forming hbond with >> 2 different acceptors/donors at different points of time >> in the trajectory. >> >> Thanks >> kavya >> -- gmx-users mailing list [email protected] >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
